Abstract
Biotic stress in legume crops is one of the major threats to crop yield and productivity. Being sessile organisms, plants have evolved a myriad of mechanisms to combat different stresses imposed on them. One such mechanism, deciphered in the last decade, is small RNA (sRNA) mediated defense in plants. Small RNAs (sRNAs) have emerged as one of the major players in gene expression regulation in plants during developmental stages and under stress conditions. They are known to act both at transcriptional and post-transcriptional levels. Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDR) constitute the major components of sRNA biogenesis machinery and are known to play a significant role in combating biotic and abiotic stresses. This study is, therefore, focused on identification and characterization of sRNA biogenesis proteins in three important legume crops, namely chickpea, pigeonpea, and groundnut. Phylogenetic analysis of these proteins between legume species classified them into distinct clades and suggests the evolutionary conservation of these genes across the members of Papillionidoids subfamily. Variable expression of sRNA biogenesis genes in response to the biotic stresses among the three legumes indicate the possible existence of specialized regulatory mechanisms in different legumes. This is the first ever study to understand the role of sRNA biogenesis genes in response to pathogen attacks in the studied legumes.
Highlights
Among the legume crops, chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), and groundnut (Arachis hypogaea) are the major crops catering to the needs of the underprivileged living in the semi-arid tropics of the world
Two different approaches were used for genome-wide identification of the DCL, AGO, and RNA dependent RNA polymerase (RDR) proteins: (i) In the first approach, the previously identified small RNA (sRNA) biogenesis protein sequences from Arabidopsis, rice, and soybean (Liu et al, 2014) were searched against the predicted gene models of chickpea, pigeonpea and groundnut using blastp program at an E-value threshold of 10−5; (ii) In parallel, the Hidden Markov Model (HMM) profiles of the domains with sRNA Biogenesis Genes in Legumes respect to DCL, AGO and RDR were downloaded from Pfam database and scanned against the predicted gene models of the legumes under study using Hmmer v 2.1.1 (Eddy, 2011)
Sterility Mosaic Disease (SMD) Infection in Pigeonpea In order to investigate the role of sRNA biogenesis genes in viral defense, we studied the expression profile of 21 genes including DCLs (4), AGOs (12), and RDRs (5)
Summary
Chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), and groundnut (Arachis hypogaea) are the major crops catering to the needs of the underprivileged living in the semi-arid tropics of the world. Chickpea, being a rich source of carbohydrates, proteins, and vitamins, is of great importance from nutrition and fodder perspectives. With an annual sRNA Biogenesis Genes in Legumes global production of ∼14.23 Mt, chickpea is ranked as the second most important legume after soybean (FAO, 2014). Its production is vastly affected by several biotic stresses, including Ascochyta blight (AB) and Fusarium wilt (FW), which may cause grain yield and quality losses of up to 100% (Navas-Cortés et al, 2000; Pande et al, 2005). AB is regarded as the most destructive foliar disease of chickpea. The economic consequence of the disease is evident from the frequent epidemics occurring in many chickpea growing areas (Pande et al, 2005)
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